SeeDB: a simple and morphology-preserving optical clearing agent for neuronal circuit reconstruction (original) (raw)
Tsai, P.S. et al. Correlations of neuronal and microvascular densities in murine cortex revealed by direct counting and colocalization of nuclei and vessels. J. Neurosci.29, 14553–14570 (2009). ArticleCAS Google Scholar
Helmchen, F. & Denk, W. Deep tissue two-photon microscopy. Nat. Methods2, 932–940 (2005). ArticleCAS Google Scholar
Tuchin, V. Tissue Optics: Light Scattering Methods and Instruments for Medical Diagnosis, 2nd edn. (SPIE Press, 2007).
Dent, J.A., Polson, A.G. & Klymkowsky, M.W. A whole-mount immunocytochemical analysis of the expression of the intermediate filament protein vimentin in Xenopus. Development105, 61–74 (1989). CASPubMed Google Scholar
Dodt, H.U. et al. Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain. Nat. Methods4, 331–336 (2007). ArticleCAS Google Scholar
Staudt, T., Lang, M.C., Medda, R., Engelhardt, J. & Hell, S.W. 2,2′-thiodiethanol: a new water soluble mounting medium for high resolution optical microscopy. Microsc. Res. Tech.70, 1–9 (2007). ArticleCAS Google Scholar
Gonzalez-Bellido, P.T. & Wardill, T.J. Labeling and confocal imaging of neurons in thick invertebrate tissue samples. Cold Spring Harb. Protoc. published online, http://dx.doi.org/doi:10.1101/pdb.prot069625 (1 September 2012).
Becker, K., Jahrling, N., Saghafi, S., Weiler, R. & Dodt, H.U. Chemical clearing and dehydration of GFP expressing mouse brains. PLoS ONE7, e33916 (2012). ArticleCAS Google Scholar
Ertürk, A. et al. Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury. Nat. Med.18, 166–171 (2012). Article Google Scholar
Taylor, W.R. An enzyme method of clearing and staining small vertebrates. Proc. USA Natl. Museum122, 1–17 (1967). Article Google Scholar
Dingerkus, G. & Uhler, L.D. Enzyme clearing of alcian blue stained whole small vertebrates for demonstration of cartilage. Stain Technol.52, 229–232 (1977). ArticleCAS Google Scholar
Hama, H. et al. Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain. Nat. Neurosci.14, 1481–1488 (2011). ArticleCAS Google Scholar
Klymkowsky, M.W. & Hanken, J. Whole-mount staining of Xenopus and other vertebrates. Methods Cell Biol.36, 419–441 (1991). ArticleCAS Google Scholar
Bancroft, J.D. & Gamble, M. Theory and Practice of Histological Techniques (Churchill Livingstone, 2007).
Dills, W.L. Jr. Protein fructosylation: fructose and the Maillard reaction. Am. J. Clin. Nutr.58, 779S–787S (1993). ArticleCAS Google Scholar
Feng, G. et al. Imaging neuronal subsets in transgenic mice expressing multiple spectral variants of GFP. Neuron28, 41–51 (2000). ArticleCAS Google Scholar
Hofer, S. & Frahm, J. Topography of the human corpus callosum revisited–comprehensive fiber tractography using diffusion tensor magnetic resonance imaging. Neuroimage32, 989–994 (2006). Article Google Scholar
Imai, T. et al. Pre-target axon sorting establishes the neural map topography. Science325, 585–590 (2009). ArticleCAS Google Scholar
Nishikimi, M., Oishi, K., Tabata, H., Torii, K. & Nakajima, K. Segregation and pathfinding of callosal axons through EphA3 signaling. J. Neurosci.31, 16251–16260 (2011). ArticleCAS Google Scholar
Schoppa, N.E. & Westbrook, G.L. Glomerulus-specific synchronization of mitral cells in the olfactory bulb. Neuron31, 639–651 (2001). ArticleCAS Google Scholar
Murthy, V.N. Olfactory maps in the brain. Annu. Rev. Neurosci.34, 233–258 (2011). ArticleCAS Google Scholar
Nagayama, S. et al. In vivo simultaneous tracing and Ca2+ imaging of local neuronal circuits. Neuron53, 789–803 (2007). ArticleCAS Google Scholar
Potter, S.M. et al. Structure and emergence of specific olfactory glomeruli in the mouse. J. Neurosci.21, 9713–9723 (2001). ArticleCAS Google Scholar
Orona, E., Rainer, E.C. & Scott, J.W. Dendritic and axonal organization of mitral and tufted cells in the rat olfactory bulb. J. Comp. Neurol.226, 346–356 (1984). ArticleCAS Google Scholar
Ghosh, S. et al. Sensory maps in the olfactory cortex defined by long-range viral tracing of single neurons. Nature472, 217–220 (2011). ArticleCAS Google Scholar
Igarashi, K.M. et al. Parallel mitral and tufted cell pathways route distinct odor information to different targets in the olfactory cortex. J. Neurosci.32, 7970–7985 (2012). ArticleCAS Google Scholar
Mori, K., Kishi, K. & Ojima, H. Distribution of dendrites of mitral, displaced mitral, tufted, and granule cells in the rabbit olfactory bulb. J. Comp. Neurol.219, 339–355 (1983). ArticleCAS Google Scholar
Nagayama, S. et al. Differential axonal projection of mitral and tufted cells in the mouse main olfactory system. Front. Neural Circuits4, 120 (2010). Article Google Scholar
Sosulski, D.L., Bloom, M.L., Cutforth, T., Axel, R. & Datta, S.R. Distinct representations of olfactory information in different cortical centres. Nature472, 213–216 (2011). ArticleCAS Google Scholar
Kim, D.H. et al. Lateral connectivity in the olfactory bulb is sparse and segregated. Front. Neural Circuits5, 5 (2011). Article Google Scholar
Orona, E., Scott, J.W. & Rainer, E.C. Different granule cell populations innervate superficial and deep regions of the external plexiform layer in rat olfactory bulb. J. Comp. Neurol.217, 227–237 (1983). ArticleCAS Google Scholar
Fantana, A.L., Soucy, E.R. & Meister, M. Rat olfactory bulb mitral cells receive sparse glomerular inputs. Neuron59, 802–814 (2008). ArticleCAS Google Scholar
Chung, K. et al. Structural and molecular interrogation of intact biological systems. Nature497, 332–337 (2013). ArticleCAS Google Scholar
Kazama, H. & Wilson, R.I. Origins of correlated activity in an olfactory circuit. Nat. Neurosci.12, 1136–1144 (2009). ArticleCAS Google Scholar
Chen, T.W., Lin, B.J. & Schild, D. Odor coding by modules of coherent mitral/tufted cells in the vertebrate olfactory bulb. Proc. Natl. Acad. Sci. USA106, 2401–2406 (2009). ArticleCAS Google Scholar
Kaplan, M.S., McNelly, N.A. & Hinds, J.W. Population dynamics of adult-formed granule neurons of the rat olfactory bulb. J. Comp. Neurol.239, 117–125 (1985). ArticleCAS Google Scholar
Hinds, J.W. & McNelly, N.A. Aging of the rat olfactory bulb: growth and atrophy of constituent layers and changes in size and number of mitral cells. J. Comp. Neurol.72, 345–367 (1977). ArticleCAS Google Scholar
Dhawale, A.K., Hagiwara, A., Bhalla, U.S., Murthy, V.N. & Albeanu, D.F. Non-redundant odor coding by sister mitral cells revealed by light addressable glomeruli in the mouse. Nat. Neurosci.13, 1404–1412 (2010). ArticleCAS Google Scholar
Kikuta, S., Fletcher, M.L., Homma, R., Yamasoba, T. & Nagayama, S. Odorant response properties of individual neurons in an olfactory glomerular module. Neuron77, 1122–1135 (2013). ArticleCAS Google Scholar
Miyasaka, N. et al. From the olfactory bulb to higher brain centers: genetic visualization of secondary olfactory pathways in zebrafish. J. Neurosci.29, 4756–4767 (2009). ArticleCAS Google Scholar
Miyamichi, K. et al. Cortical representations of olfactory input by trans-synaptic tracing. Nature472, 191–196 (2011). ArticleCAS Google Scholar
Yu, Y.C. et al. Preferential electrical coupling regulates neocortical lineage-dependent microcircuit assembly. Nature486, 113–117 (2012). ArticleCAS Google Scholar
Li, Y. et al. Clonally related visual cortical neurons show similar stimulus feature selectivity. Nature486, 118–121 (2012). ArticleCAS Google Scholar
Ohtsuki, G. et al. Similarity of visual selectivity among clonally related neurons in visual cortex. Neuron75, 65–72 (2012). ArticleCAS Google Scholar
Livet, J. et al. Transgenic strategies for combinatorial expression of fluorescent proteins in the nervous system. Nature450, 56–62 (2007). ArticleCAS Google Scholar
Marshel, J.H., Mori, T., Nielsen, K.J. & Callaway, E.M. Targeting single neuronal networks for gene expression and cell labeling in vivo. Neuron67, 562–574 (2010). ArticleCAS Google Scholar
Lo, L. & Anderson, D.J.A. Cre-dependent, anterograde transsynaptic viral tracer for mapping output pathways of genetically marked neurons. Neuron72, 938–950 (2011). ArticleCAS Google Scholar
Kim, J. et al. mGRASP enables mapping mammalian synaptic connectivity with light microscopy. Nat. Methods9, 96–102 (2012). ArticleCAS Google Scholar
Lin, D.M. et al. Formation of precise connections in the olfactory bulb occurs in the absence of odorant-evoked neuronal activity. Neuron26, 69–80 (2000). ArticleCAS Google Scholar
Saito, T. In vivo electroporation in the embryonic mouse central nervous system. Nat. Protoc.1, 1552–1558 (2006). ArticleCAS Google Scholar